tricc-oo 1.5.21__py3-none-any.whl → 1.5.23__py3-none-any.whl

tests/build.py

@@ -1,3 +1,9 @@
+from tricc_oo.strategies.output.spice import SpiceStrategy
+from tricc_oo.strategies.output.xlsform_cht_hf import XLSFormCHTHFStrategy
+from tricc_oo.strategies.output.xlsform_cht import XLSFormCHTStrategy
+from tricc_oo.strategies.output.xlsform_cdss import XLSFormCDSSStrategy
+from tricc_oo.strategies.output.xls_form import XLSFormStrategy
+from tricc_oo.strategies.input.drawio import DrawioStrategy
 import getopt
 import gettext
 import logging
@@ -23,15 +29,9 @@ langs = SingletonLangClass()
 # langs.add_trad('fr', fr)
 # langs.add_trad('en', en)
 
-from tricc_oo.strategies.input.drawio import DrawioStrategy
 
 # from tricc_oo.serializers.medalcreator import execute
 
-from tricc_oo.strategies.output.xls_form import XLSFormStrategy
-from tricc_oo.strategies.output.xlsform_cdss import XLSFormCDSSStrategy
-from tricc_oo.strategies.output.xlsform_cht import XLSFormCHTStrategy
-from tricc_oo.strategies.output.xlsform_cht_hf import XLSFormCHTHFStrategy
-from tricc_oo.strategies.output.spice import SpiceStrategy
 
 def setup_logger(
     logger_name,
@@ -94,9 +94,7 @@ LEVELS = {
 
 
 def print_help():
-    print(
-        "-i / --input draw.io filepath (MANDATORY) or directory containing drawio files"
-    )
+    print("-i / --input draw.io filepath (MANDATORY) or directory containing drawio files")
     print("-o / --output xls file ")
     print("-d form_id ")
     print("-s L4 system/strategy (odk, cht, cc)")
@@ -116,9 +114,7 @@ if __name__ == "__main__":
     input_strategy = "DrawioStrategy"
     output_strategy = "XLSFormStrategy"
     try:
-        opts, args = getopt.getopt(
-            sys.argv[1:], "hti:o:s:I:O:l:d:D:", ["input=", "output=", "help", "trads"]
-        )
+        opts, args = getopt.getopt(sys.argv[1:], "hti:o:s:I:O:l:d:D:", ["input=", "output=", "help", "trads"])
     except getopt.GetoptError:
         print_help()
         sys.exit(1)
@@ -145,7 +141,7 @@ if __name__ == "__main__":
     if in_filepath is None:
         print_help()
         sys.exit(2)
-    
+
     if not download_dir:
         download_dir = out_path
     debug_path = os.fspath(out_path + "/debug.log")
@@ -165,7 +161,7 @@ if __name__ == "__main__":
         setup_logger("default", debug_file_path, logging.INFO)
     file_content = []
     files = []
-    in_filepath_list = in_filepath.split(',')
+    in_filepath_list = in_filepath.split(",")
     for in_filepath in in_filepath_list:
         pre, ext = os.path.splitext(in_filepath)
 
@@ -173,18 +169,13 @@ if __name__ == "__main__":
             # if output file path not specified, just chagne the extension
             out_path = os.path.dirname(pre)
 
-
         if os.path.isdir(in_filepath):
-            files = [
-                os.path.join(in_filepath, f)
-                for f in os.listdir(in_filepath) 
-                if f.endswith(".drawio")
-            ]
+            files = [os.path.join(in_filepath, f) for f in os.listdir(in_filepath) if f.endswith(".drawio")]
         elif os.path.isfile(in_filepath) and in_filepath.endswith(".drawio"):
             files = [in_filepath]
-            
+
         for f in files:
-            with open(f, 'r') as s:
+            with open(f, "r") as s:
                 content = s.read()
                 # present issue with some drawio file that miss the XML header
 
@@ -193,7 +184,6 @@ if __name__ == "__main__":
         logger.critical(f"{in_filepath} is neither a drawio file nor a directory containing drawio files")
         exit(1)
 
-
     strategy = globals()[input_strategy](files)
     logger.info(f"build the graph from strategy {input_strategy}")
     media_path = os.path.join(out_path, "media-tmp")

tests/test_cql.py

@@ -1,61 +1,40 @@
 import unittest
 
-from tricc_oo.converters.cql_to_operation import cqlToXlsFormVisitor, transform_cql_to_operation
-from tricc_oo.models.base import  TriccOperator, TriccOperation, TriccStatic, TriccReference
+from tricc_oo.converters.cql_to_operation import transform_cql_to_operation
+from tricc_oo.models.base import TriccOperator, TriccOperation, TriccStatic, TriccReference
+
 
 class TestCql(unittest.TestCase):
     def test_and(self):
-        if_cql = "\"p_weight\" is not null and \"p_age\" > 2"
+        if_cql = '"p_weight" is not null and "p_age" > 2'
         dg_operation = transform_cql_to_operation(if_cql)
         dg_expected = TriccOperation(
             operator=TriccOperator.AND,
             reference=[
-                TriccOperation(
-                    operator=TriccOperator.ISNOTNULL,
-                    reference=[TriccReference("p_weight")]
-                ),
-                TriccOperation(
-                    operator=TriccOperator.MORE,
-                    reference=[
-                        TriccReference("p_age"),
-                        TriccStatic(
-                            value=2
-                        )
-                    ]
-                )
-            ]
+                TriccOperation(operator=TriccOperator.ISNOTNULL, reference=[TriccReference("p_weight")]),
+                TriccOperation(operator=TriccOperator.MORE, reference=[TriccReference("p_age"), TriccStatic(value=2)]),
+            ],
         )
         self.assertEqual(str(dg_operation), str(dg_expected))
-    
-   
+
     def test_durg_doage(self):
-        if_cql = "DrugDosage('paracetamol', \"p_weight\", \"p_age\")"
+        if_cql = 'DrugDosage(\'paracetamol\', "p_weight", "p_age")'
         dg_operation = transform_cql_to_operation(if_cql)
         dg_expected = TriccOperation(
             operator=TriccOperator.DRUG_DOSAGE,
-            reference=[
-                TriccStatic(value='paracetamol'),
-                TriccReference("p_weight"),
-                TriccReference("p_age")
-            ]
+            reference=[TriccStatic(value="paracetamol"), TriccReference("p_weight"), TriccReference("p_age")],
         )
         self.assertEqual(str(dg_operation), str(dg_expected))
-    
+
     def test_implied_concat(self):
         if_cql = "'A' & \"B\" & 'C'"
         cc_operation = transform_cql_to_operation(if_cql)
         cc_expected = TriccOperation(
             operator=TriccOperator.CONCATENATE,
-            reference=[
-                TriccStatic(value='A'),
-                TriccReference("B"),
-                TriccStatic(value='C')
-            ]
+            reference=[TriccStatic(value="A"), TriccReference("B"), TriccStatic(value="C")],
         )
         self.assertEqual(str(cc_operation), str(cc_expected))
-    
-    
-    
+
     def test_if(self):
         if_cql = "if AgeInDays() < 60 then 'newborn' else 'child'"
         if_operation = transform_cql_to_operation(if_cql)
@@ -64,19 +43,11 @@ class TestCql(unittest.TestCase):
             reference=[
                 TriccOperation(
                     operator=TriccOperator.LESS,
-                    reference=[
-                        TriccOperation(
-                            operator=TriccOperator.AGE_DAY,
-                            reference=[]
-                        ),
-                        TriccStatic(
-                            value=60
-                        )
-                    ]
+                    reference=[TriccOperation(operator=TriccOperator.AGE_DAY, reference=[]), TriccStatic(value=60)],
                 ),
-                TriccStatic(value='newborn'),
-                TriccStatic(value='child'),
-            ]
+                TriccStatic(value="newborn"),
+                TriccStatic(value="child"),
+            ],
         )
         self.assertEqual(str(if_operation), str(if_expected))
 
@@ -91,28 +62,11 @@ class TestCql(unittest.TestCase):
         case_expected = TriccOperation(
             operator=TriccOperator.CASE,
             reference=[
-                TriccOperation(
-                    operator=TriccOperator.AGE_MONTH,
-                    reference=[]
-                ),
-                [
-                    TriccStatic(
-                        value=0
-                    ),
-                    TriccStatic(
-                        value="newborn"
-                    )
-                ],
-                [
-                    TriccStatic(
-                        value=1
-                    ),
-                    TriccStatic(
-                        value="newborn"
-                    )
-                ],
-                TriccStatic(value='child'),
-            ]
+                TriccOperation(operator=TriccOperator.AGE_MONTH, reference=[]),
+                [TriccStatic(value=0), TriccStatic(value="newborn")],
+                [TriccStatic(value=1), TriccStatic(value="newborn")],
+                TriccStatic(value="child"),
+            ],
         )
         self.assertEqual(str(case_operation), str(case_expected))
 
@@ -131,57 +85,32 @@ class TestCql(unittest.TestCase):
                     TriccOperation(
                         operator=TriccOperator.LESS_OR_EQUAL,
                         reference=[
-                            TriccOperation(
-                                operator=TriccOperator.AGE_MONTH,
-                                reference=[]
-                            ),
-                            TriccStatic(
-                                value=2
-                            )
-                        ]
+                            TriccOperation(operator=TriccOperator.AGE_MONTH, reference=[]),
+                            TriccStatic(value=2),
+                        ],
                     ),
-                    TriccStatic(
-                        value=True
-                    )
+                    TriccStatic(value=True),
                 ],
                 [
                     TriccOperation(
                         operator=TriccOperator.MORE,
-                        reference=[
-                            TriccOperation(
-                                operator=TriccOperator.AGE_YEAR,
-                                reference=[]
-                            ),
-                            TriccStatic(
-                                value=5
-                            )
-                        ]
+                        reference=[TriccOperation(operator=TriccOperator.AGE_YEAR, reference=[]), TriccStatic(value=5)],
                     ),
-                    TriccStatic(
-                        value=True
-                    )
+                    TriccStatic(value=True),
                 ],
                 TriccStatic(value=False),
-            ]
+            ],
         )
         self.assertEqual(str(case_operation), str(case_expected))
 
-
     def test_minus(self):
-        minus_cql =""" "WFL" >= -3"""
+        minus_cql = """ "WFL" >= -3"""
         # minus_cql = """
         # ("age_in_months" < 6 and "WFL" >= -3 and "WFL" < -2) is true
         # """
         minus_operation = transform_cql_to_operation(minus_cql)
         minus_expected = TriccOperation(
-            TriccOperator.MORE_OR_EQUAL,
-            [
-                TriccReference("WFL"),
-                TriccOperation(
-                    TriccOperator.MINUS,
-                    [TriccStatic(3)]
-                )
-            ]
+            TriccOperator.MORE_OR_EQUAL, [TriccReference("WFL"), TriccOperation(TriccOperator.MINUS, [TriccStatic(3)])]
         )
         self.assertEqual(str(minus_operation), str(minus_expected))
 
@@ -195,13 +124,13 @@ class TestCql(unittest.TestCase):
                     operator=TriccOperator.SELECTED,
                     reference=[
                         TriccReference("identifier"),
-                        TriccStatic(value='code'),
-                    ]
+                        TriccStatic(value="code"),
+                    ],
                 )
-            ]
+            ],
         )
         self.assertEqual(str(dg_operation), str(dg_expected))
-    
 
-if __name__ == '__main__':
-    unittest.main()
+
+if __name__ == "__main__":
+    unittest.main()

tests/to_ocl.py

@@ -1,51 +1,49 @@
-import os
 import json
 from pathlib import Path
 from tricc_oo.converters.codesystem_to_ocl import transform_fhir_to_ocl
 
+
 def find_and_process_codesystems(directory_path):
     # Convert string path to Path object if not already
     dir_path = Path(directory_path)
-    
+
     # Find all JSON files in the directory
     for json_file in dir_path.glob("*.json"):
         try:
             # Read the JSON file
-            with open(json_file, 'r', encoding='utf-8') as f:
+            with open(json_file, "r", encoding="utf-8") as f:
                 data = json.load(f)
-                
+
                 # Check if resource_type is CodeSystem
                 if data.get("resourceType") == "CodeSystem":
                     # Get the filename without extension for output naming
                     file_key = json_file.stem
-                    
+
                     # Write the original CodeSystem JSON
                     output_cs_path = dir_path / f"{file_key}_codesystem.json"
-                    with open(output_cs_path, "w", encoding='utf-8') as file:
+                    with open(output_cs_path, "w", encoding="utf-8") as file:
                         file.write(json.dumps(data, indent=4))
-                    
+
                     # Transform to OCL payload
                     ocl_payload = transform_fhir_to_ocl(
-                        data,
-                        source_name="ALM",
-                        source_owner="pdelcroix",
-                        source_owner_type="User"
+                        data, source_name="ALM", source_owner="pdelcroix", source_owner_type="User"
                     )
-                    
+
                     # Save the transformed OCL payload
                     output_ocl_path = dir_path / f"{file_key}_ocl_bulk_upload.json"
-                    with open(output_ocl_path, "w", encoding='utf-8') as f:
+                    with open(output_ocl_path, "w", encoding="utf-8") as f:
                         for item in ocl_payload:
                             json_line = json.dumps(item.dict(exclude_none=True))
-                            f.write(json_line + '\n')
-                    
+                            f.write(json_line + "\n")
+
                     print(f"OCL bulk upload payload generated successfully for {file_key}!")
-                    
+
         except json.JSONDecodeError:
             print(f"Error: Invalid JSON in file {json_file}")
         except Exception as e:
             print(f"Error processing {json_file}: {str(e)}")
 
+
 # Example usage
 media_path = "path/to/your/directory"  # Replace with your directory path
-find_and_process_codesystems(media_path)
+find_and_process_codesystems(media_path)

tricc_oo/__init__.py

@@ -5,9 +5,3 @@ Collect easy.
 """
 
 __version__ = "1.0.2"
-
-from .models.base import *
-from .models.calculate import *
-from .models.tricc import *
-from .serializers import *
-

tricc_oo/converters/codesystem_to_ocl.py

@@ -1,5 +1,4 @@
 from typing import Dict, List, Any
-import json
 from fhir.resources.codesystem import CodeSystem
 from tricc_oo.models.ocl import (
     OCLConcept,
@@ -7,15 +6,16 @@ from tricc_oo.models.ocl import (
     OCLDetailedName,
     OCLDetailedDescription,
     OclConstants,
-    get_data_type
 )
 
+
 def extract_properties_metadata(fhir_cs: CodeSystem) -> Dict[str, Dict]:
     """
-    Extracts property definitions from FHIR CodeSystem and converts them to OCL attribute types
+    Extracts property definitions from FHIR CodeSystem and converts them
+    to OCL attribute types
     """
     property_types = {}
-    if hasattr(fhir_cs, 'property') and fhir_cs.property:
+    if hasattr(fhir_cs, "property") and fhir_cs.property:
         for prop in fhir_cs.property:
             # Map FHIR property types to OCL datatypes
             fhir_type = prop.type
@@ -26,76 +26,85 @@ def extract_properties_metadata(fhir_cs: CodeSystem) -> Dict[str, Dict]:
                 "decimal": "Numeric",
                 "integer": "Numeric",
                 "dateTime": "DateTime",
-                "string": "Text"
+                "string": "Text",
             }.get(fhir_type, "Text")
-            
+
             property_types[prop.code] = {
                 "name": prop.code,
                 "datatype": ocl_type,
-                "description": prop.description if hasattr(prop, 'description') else ""
+                "description": prop.description if hasattr(prop, "description") else "",
             }
     return property_types
 
+
 def get_fhir_concept_datatype(concept):
-    
-    datatype = extract_concept_properties(concept, ['datatype'])
+    datatype = extract_concept_properties(concept, ["datatype"])
     if datatype:
-        return datatype['datatype']
+        return datatype["datatype"]
     else:
         return OclConstants.DATA_TYPE_NONE
 
+
 def extract_concept_properties(concept, property_types: List) -> List[Dict]:
     """
     Extracts properties from a FHIR concept and converts them to OCL attributes
     """
     properties = {}
-    if hasattr(concept, 'property') and concept.property:
+    if hasattr(concept, "property") and concept.property:
         for prop in concept.property:
             if prop.code in property_types:
                 # Handle different property value types
-                if getattr(prop, 'valueCode', None):
+                if getattr(prop, "valueCode", None):
                     value = prop.valueCode
-                elif getattr(prop, 'valueCoding', None):
+                elif getattr(prop, "valueCoding", None):
                     value = prop.valueCoding.code
-                elif getattr(prop, 'valueString', None):
+                elif getattr(prop, "valueString", None):
                     value = prop.valueString
-                elif getattr(prop, 'valueBoolean', None):
+                elif getattr(prop, "valueBoolean", None):
                     value = prop.valueBoolean
-                elif getattr(prop, 'valueInteger', None):
+                elif getattr(prop, "valueInteger", None):
                     value = prop.valueInteger
-                elif getattr(prop, 'valueDecimal', None):
+                elif getattr(prop, "valueDecimal", None):
                     value = prop.valueDecimal
-                elif getattr(prop, 'valueDateTime', None):
+                elif getattr(prop, "valueDateTime", None):
                     value = prop.valueDateTime
                 else:
                     continue
                 if value:
                     properties[prop.code] = value
     return properties
-                
-                
+
+
 def get_attributes_from_concept_properties(concept, property_types: Dict) -> List[Dict]:
     attributes = []
     properties = extract_concept_properties(concept, property_types=list(property_types))
     for code, value in properties.items():
-        attributes.append({
-            "type": "Attribute",
-            "attribute_type": code,
-            "value": value,
-            "value_type": property_types[code]["datatype"]
-        })
+        attributes.append(
+            {
+                "type": "Attribute",
+                "attribute_type": code,
+                "value": value,
+                "value_type": property_types[code]["datatype"],
+            }
+        )
     return attributes
 
-def transform_fhir_to_ocl(fhir_codesystem_json: Dict, source_name: str, source_owner: str, source_owner_type: str) -> List[Dict[str, Any]]:
+
+def transform_fhir_to_ocl(
+    fhir_codesystem_json: Dict,
+    source_name: str,
+    source_owner: str,
+    source_owner_type: str,
+) -> List[Dict[str, Any]]:
     """
     Transforms a FHIR CodeSystem resource into an OCL bulk upload JSON payload.
-    
+
     Args:
         fhir_codesystem_json: JSON representation of the FHIR CodeSystem resource
         source_name: Name of the OCL Source
         source_owner: Owner of the OCL Source (organization or user)
         source_owner_type : User or Organization
-    
+
     Returns:
         List of dictionaries representing OCL bulk upload format
     """
@@ -109,8 +118,7 @@ def transform_fhir_to_ocl(fhir_codesystem_json: Dict, source_name: str, source_o
     ocl_payload = []
 
     # Add source metadata
-
-    
+    source_extras = {}
     # Add property definitions to extras
     if property_types:
         source_extras["attribute_types"] = list(property_types.values())
@@ -123,16 +131,17 @@ def transform_fhir_to_ocl(fhir_codesystem_json: Dict, source_name: str, source_o
             owner=source_owner,
             owner_type=source_owner_type,
             name=fhir_cs.name or "Unnamed Source",
-            full_name=fhir_cs.title if hasattr(fhir_cs, 'title') else fhir_cs.name,
+            full_name=fhir_cs.title if hasattr(fhir_cs, "title") else fhir_cs.name,
             description=fhir_cs.description or "",
             source_type="Dictionary",
             default_locale="en",
             supported_locales=["en"],
+            extras=source_extras,
         )
-      )
+    )
 
     # Transform concepts
-    if hasattr(fhir_cs, 'concept') and fhir_cs.concept:
+    if hasattr(fhir_cs, "concept") and fhir_cs.concept:
         for concept in fhir_cs.concept:
             datatype = get_fhir_concept_datatype(concept)
             ocl_concept = OCLConcept(
@@ -149,15 +158,17 @@ def transform_fhir_to_ocl(fhir_codesystem_json: Dict, source_name: str, source_o
                         name_type=OclConstants.NAME_TYPE_FULLY_SPECIFIED,
                     )
                 ],
-                descriptions=[]
+                descriptions=[],
             )
 
             # Add definition if present
-            if hasattr(concept, 'definition') and concept.definition:
-                ocl_concept.descriptions.append(OCLDetailedDescription(
-                    description=concept.definition,
-                    locale="en",
-                ))
+            if hasattr(concept, "definition") and concept.definition:
+                ocl_concept.descriptions.append(
+                    OCLDetailedDescription(
+                        description=concept.definition,
+                        locale="en",
+                    )
+                )
 
             # Extract and add properties as attributes
             attributes = get_attributes_from_concept_properties(concept, property_types)

tricc_oo/converters/cql/cqlLexer.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 # Generated from cql.g4 by ANTLR 4.13.2
 from antlr4 import *
 from io import StringIO

tricc_oo/converters/cql/cqlListener.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 # Generated from cql.g4 by ANTLR 4.13.2
 from antlr4 import *
 if "." in __name__:

tricc_oo/converters/cql/cqlParser.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 # Generated from cql.g4 by ANTLR 4.13.2
 # encoding: utf-8
 from antlr4 import *

tricc_oo/converters/cql/cqlVisitor.py

@@ -1,3 +1,4 @@
+# flake8: noqa
 # Generated from cql.g4 by ANTLR 4.13.2
 from antlr4 import *
 if "." in __name__: